unique peptide output with position on proteins

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@370 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java

@@ -38,6 +38,7 @@ import fr.inra.pappso.xtandempipeline.class_msms.Match;
 import fr.inra.pappso.xtandempipeline.class_msms.Protein;
 import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
 import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.HashPeptideSet;
 import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
 import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
 
@@ -94,11 +95,15 @@ public class OdsRedundantPeptideOutput {
 						Protein prot = (Protein) hashProt.getGrpProtMatch()
 								.getGrpProtein();
 						// peptidesHitRef
+						HashPeptideSet uniquePeptideSet = new HashPeptideSet();
 						for (Peptide peptide : ((Match) hashProt
 								.getGrpProtMatch())
 								.get_peptide_order_inclus_redon()) {
 
-							this.writeOnePeptide(group, sg, prot, peptide);
+							// HashPeptide p = peptide.getHashPeptide();
+							if (uniquePeptideSet.add(peptide.getHashPeptide())) {
+								this.writeOnePeptide(group, sg, prot, peptide);
+							}
 						}
 					}
 				}
@@ -121,20 +126,21 @@ public class OdsRedundantPeptideOutput {
 			odsTable.writeCell("Subgroup");
 			odsTable.writeCell("Protein accession");
 			odsTable.writeCell("Protein description");
-			odsTable.writeCell("MS Sample");
+			odsTable.writeCell("Peptide ID");
+			// odsTable.writeCell("MS Sample");
 			odsTable.writeCell("Scan");
-			odsTable.writeCell("Rt (s)");
+			// odsTable.writeCell("Rt (s)");
 			odsTable.writeCell("Sequence");
 			odsTable.writeCell("Modifs");
 			odsTable.writeCell("Start");
 			odsTable.writeCell("Stop");
 
-			odsTable.writeCell("E-value");
-			odsTable.writeCell("Charge");
-			odsTable.writeCell("MH+ Obs");
-			odsTable.writeCell("MH+ theo");
-			odsTable.writeCell("DeltaMH+");
-			odsTable.writeCell("Delta-ppm");
+			// odsTable.writeCell("E-value");
+			// odsTable.writeCell("Charge");
+			// odsTable.writeCell("MH+ Obs");
+			// odsTable.writeCell("MH+ theo");
+			// odsTable.writeCell("DeltaMH+");
+			// odsTable.writeCell("Delta-ppm");
 		} catch (XMLStreamException e) {
 			String message = "XMLStreamException in writeHeaders() "
 					+ e.getMessage();
@@ -152,26 +158,28 @@ public class OdsRedundantPeptideOutput {
 			odsTable.writeCell(sg.getNumber());
 			odsTable.writeCell(prot.getAccession());
 			odsTable.writeCell(prot.get_description());
-			odsTable.writeCell(peptide.get_sample());
+			// odsTable.writeCell(peptide.get_sample());
+			odsTable.writeCell(peptide.getHashPeptide().getScan() + "-"
+					+ peptide.getHashPeptide().getSequence());
 			odsTable.writeCell(peptide.getSampleScan().getScan());
-			odsTable.writeCell(peptide.get_RT_in_sec());
+			// odsTable.writeCell(peptide.get_RT_in_sec());
 			odsTable.writeCell(peptide.getSequence());
 			odsTable.writeCell(peptide.get_Modifs_formater());
 			odsTable.writeCell(peptide.get_start());
 			odsTable.writeCell(peptide.get_stop());
 
-			odsTable.writeCell(peptide.get_evalue());
+			// odsTable.writeCell(peptide.get_evalue());
 			// S.append("\t" + pep.get_evalue());
-			odsTable.writeCell(peptide.get_charge());
+			// odsTable.writeCell(peptide.get_charge());
 			// S.append("\t" + pep.get_charge());
-			odsTable.writeCell(peptide.get_mhplus_obser());
+			// odsTable.writeCell(peptide.get_mhplus_obser());
 			// S.append("\t" + pep.get_mhplus_obser());
-			odsTable.writeCell(peptide.get_mhplus_theo());
+			// odsTable.writeCell(peptide.get_mhplus_theo());
 			// S.append("\t" + pep.get_mhplus_theo());
-			odsTable.writeCell(peptide.get_deltamass());
+			// odsTable.writeCell(peptide.get_deltamass());
 			// S.append("\t" + pep.get_deltamass());
-			odsTable.writeCell(((peptide.get_deltamass() / peptide
-					.get_mhplus_theo()) * 1000000));
+			// odsTable.writeCell(((peptide.get_deltamass() / peptide
+			// .get_mhplus_theo()) * 1000000));
 
 		} catch (XMLStreamException e) {
 			String message = "XMLStreamException in writeOnePeptide(Group group, SubGroup sg, Protein prot,	Peptide peptide) "